WindowView — Science

Perspectives

(092112)

Genes in Action — Mystery Link:

From genetic information to cell structure and
function

Consider This:

The point of WindowView
perspective building is to stop ourselves to pause, to ask the questions that
are obviously too often quickly swept aside. For example, a cell operates
many functions based on enzyme activities. One operation, say moving some
DNA from one location to another location on the same or other chromosome,
requires a bit of coordinated activity. It happens, that's a fact. That it
happens by several coordinated steps, by several enzymes is amazing. To plan
to move from house to house takes anticipation of multiple tasks. You can
think ahead of how the move will happen. But does a cell think? Might evolution
in advance of the existence of a cell 'know' to develop just the correct three
or so enzymes to anticipate the need to move DNA around? Furthermore, that
a cell has any ability to anticipate the need to move DNA goes beyond chance.
Science simply reports that the steps take place. But when do we get the opportunity
to be 'blown away' by the wonder of it all. Genes move about the genetic house
(i.e., within a cell's nucleus). This isn't merely happenstance... it creates
powerful adjustments to meet demands from outside the cell. The way genes
work exhibits an informational system that is incredible. Think about it!
Mechanistic explanations are not enough to account for the systems that make
us work—indeed they work in marvelous fashion. Yet the scientific journal
reports are expressionless—lacking wonder, lacking critical thinking.

Recombination
is not a simple process. We do not yet understand how the breaking
of chromosomes and the swapping of pieces is done as precisely at
is it is. We do know, though, that it is controlled by special enzymes
that break the chromosomes, exchange the pieces, and rejoin the free
ends. Spetner (NBC)
Page 39

Geneticists have
found that the inversions, deletions, insertions, and transpositions
are not just haphazard events. Special pieces of DNA that jump around
in the chromosomes cause these genetic changes. Short pieces of DNA,
called transposons, have been found to jump from place to place in
the chromosomes. They have also been found to activate other special,
shorter, pieces and make them jump as well. Spetner
(NBC) Page 42

A. transposon has
in it sections of DNA that encode to of the enzymes in it needs to
carry out its job.

But because no
one knows why they occur, many geneticists have assumed they occur
only by chance. I find it hard to believe that a process as precise
and as well controlled as the transposition of genetic elements happens
only by chance. Some scientists tend to call a mechanism random before we learned what it really does. If the source of the variation
for evolution were point mutations, we could say the variation is
random. But if the source of the variation is the complex process
of transposition, and then there is no justification for saying that
evolution is based on random events. I'll return to this subject in
Chapter 5 and again in Chapter 7. Spetner
(NBC) Page 44

Neo-Darwinism
is elegantly simple. The theory can be summarized in four propositions:
every organism develops according to a program encoded in its genes
(which is to say, its DNA); DNA is the hereditary material that transmits
traits from organisms to their descendants; new traits occasionally
arise because of DNA mutations; and natural selection produces both
microevolution (within a species or genus) and macroevolution (above
the species or genus level) by favoring advantageous traits and thereby
increasing the frequency of their genes in the population. Wells
(MC) Page 51

The
modern synthesis of Darwin's theory with population and molecular
genetics, however, left out embryology. Embryology was "second to
none in importance" for Darwin, and along with homology provided him
with such convincing evidence for descent with modification that he
would have adopted this theory "even if it were unsupported by other
facts or arguments" (Darwin 1936, 346, 352). Yet embryology was virtually
ignored by the modern synthesis (Bowler 1989; Gilbert 1994; Sapp 1987). Wells (MC) Page 52

Darwin had noted
that vertebrate embryos resemble each other at a certain stage in
their development and considered this resemblance to be evidence of
common ancestry. In fact, however, in the early stages of their development
vertebrate embryos are radically different from each other. In the
1980s comparative embryologists began to find many cases in which
organisms with very similar morphologies follow radically dissimilar
pathways in early development. Rather than regarding this as a threat
to Darwin's theory, evolutionary biologists are now interpreting it
as evidence that early development can be easily modified to produce
macroevolutionary change.

Thus developmental
genetics seems to have provided empirical confirmation of the neo-Darwinian
proposition that organisms develop according to a program encoded
in their DNA that evolved from a common ancestor through mutation
and natural selection. And comparative embryology seems to have provided
evidence that major changes in the early development are relatively
easy to achieve. According to a recent review of the advances in evolutionary
and developmental biology, "the evidence for evolution is better than
ever" (Gilbert, Opitz, and Raff 1996, 368).

Or is it? In the
opinion of some biologists, myself included, recent discoveries in
developmental genetics and comparative embryology pose serious problems
for neo-Darwinism. Those discoveries have been welcomed into the City
of Darwin, but I predict that, like a Trojan horse, they will bring
that city down. To illustrate my point I will survey recent data about
homeotic genes, which neo-Darwinists consider to be their best evidence
that evolution modifies development by altering genetic programs,
and show that those data raise more questions than they answer. Wells (MC) Page 52

It
seems as though the neo-Darwinian proposition that "novel morphological
forms in animal evolution result from changes in genetically encoded
programs of developmental regulation" (Davidson, Peterson and Cameron
1995, 1319) has been empirically confirmed.

Or has
it? Although most Darwinian biologists have not yet realized it, the
very universality of homeotic genes invalidates the grand claims that
are made for them. Here is why: if biological structures are determined
by their genes, then different structures must be determined by different
genes. If the same gene can "determine" structures as radically different
as a fruit fly's leg and a mouse's brain or and insect's eyes and
the eyes of humans and squids, then that gene is not determining a
much of anything.Wells (MC) Page 56

Similarly, except
for telling us how an embryo directs its cells into one of several
built-in developmental pathways, homeotic genes tell us nothing about
how biological structures are formed.

In other words,
the universality of homeotic genes is supposed to be due to their
presence in a common ancestor, but the preponderance of the evidence
suggests that the common ancestor lacked the features that those homeotic
genes now supposedly control. From a Darwinian perspective this is
a serious problem. According to neo-Darwinism, complex gene sequences
gradually evolve by conferring selective advantages on the organisms
that possess them. The gene sequences confer selective advantages
only if they program the development of useful adaptations. If a primitive
animal possessed homeotic genes but lacked all the adaptations now
associated with them, then those genes must have originated prior
to those adaptations. How then did homeotic genes evolve? Wells
(MC) Page 57

The bottom line
is that each new piece of evidence demonstrating the universality
of homeotic genes (and thus their independence from any particular
adaptation) makes their presence in a putative common ancestor more
difficult for neo-Darwinists to explain. Ironically the very discoveries
that Darwinian biologists now find so exciting are adding to the list
of the difficulties for their theory.

If, instead, homeotic
genes are the product of intelligent design, this particular difficulty
disappears. Once design is admitted, there is no obstacle to saying
that a complex gene sequence can originate quickly, based upon future
rather than past usefulness, and that its designer can incorporate
it into a wide variety of organisms that otherwise share few structural
similarities. Just as an engineer would not be surprised to find similar
ignition switch is in different kinds of vehicles produced by the
same of manufacturer, so biologist who it meant design need not be
surprised to find similar homeotic genes in most all or all types
of animals.

Thus a design approach
is better able than a neo-Darwinism to accommodate a recent discoveries
in developmental genetics. The superiority of a design perspective
is also apparent in the light of recent discoveries in a comparative
embryology. Wells (MC) Page 58

Genetic Programs Or Organic
Forms?

[We assume and DNA
explains it all; but not so! ]

Although
molecular biology has demonstrated conclusively that DNA carries the
genetic code for the amino acid sequence of proteins, this is not
sufficient to specify a whole organism. Combining DNA with all the
ingredients necessary for protein synthesis does not make a cell.

Why not? Consider
the analogy of building a house. One needs to specify a and provide
the building materials: boards of particular sizes and shapes, nails,
insulation, shingles, windows, doors, electrical wires, pipes and
so on. One also needs to specify the order in which components should
be assembled, because the foundation must be completed before the
walls and roof are erected and the plumbing and wiring are installed.
Most important, one needs to specify the intended floor plan, because
the individual materials could be combined in a number of different
ways. Molecular biology has shown that an organism's DNA specifies
the building materials. It turns out, however, that the assembly instructions
are largely in other components of the cell, and that the floor plan
has not yet been discovered. Wells
(MC) Page 62

...
but the three-dimensional structure of large aggregates of these building
blocks is not determined by the structure of individual submits anymore
than the floor plan of the House is determined by the shape of its
bricks.

Consider,
for example, the cytoskeleton ...

... assembly
of these subunits into a three-dimensional structures is a dynamic
process which depends on intracellular nucleating sites and environmental
cues, ...

Thus
of the generation of shape, or morphogenesis, is not reducible to
subunit structure. Developmental biologist Brian Goodwin writes that
"genes are responsible for determining which molecules an organism
can produce" but this fails to address the basic problem posed by
morphogenesis, namely, how distinctive and spatial order are arises
in embryos." He concludes that "the molecular composition of organisms
does not, in general, determine their form" (Goodwin 1985, 32).

Shape
is not the only variable unspecified by the DNA. In multicellular
organisms, cell types differ in physiology as well as morphology.

For example,
liver cells, muscle cells and nerve cells are not only shaped differently
but also manufacture different proteins and perform very different
biochemical functions. Yet they all contain the same DNA, which they
inherited from the fertilized egg.

Whatever
is producing the differences, it must be something other than their
DNA. Developmental biologist H. F. Nijhout writes that "the only strictly
correct view of the function of genes is that they supply cells, and
ultimately organisms, with a chemical materials." Furthermore the
function of the homeotic and other regulatory genes "is ultimately
no different from that of structural genes, in that they simply provide
efficient ways of ensuring that the required materials are supplied
at the right time and place" (Nijhout 1990, 444).

...there
it is evidence that cell differentiation is due to factors that are
regionally localized in the fertilized egg. But such regional localization
precedes gene activity in the cells whose developmental pathways it
determines. Wells
(MC) Page 63

In other words,
even in those organisms in which cellular differences can be traced
directly to regional differences in the fertilized egg, the floor
plan is independent of the DNA.

If the organism's
floor plan is not in its DNA, where is it? Other features of an embryo
that can carry developmental information include the cytoskeleton,
the membrane and the cytoplasm. When a sperm and fertilizes an egg,
in many cases it transmits not only DNA but also a nucleating center,
or centrosome, for the embryonic cytoskeleton. Wells
(MC) Page 64

Experiments
with vertebrate tissues show that dividing cells transmit cytoskeletal
patterns to their descendants that determine the spatial orientation
of cells in those tissues (Locke 1990).

Membranes also
carry morphogenetic information that can be inherited independently
of DNA. Biological membranes are not merely featureless bags but included
proteins and other molecules that are spatially distributed in highly
structured patterns; and when a cell divides, its progeny inherent
not only its DNA but also a membrane pattern. Experiments with protozoa
(single-celled organisms possessing nuclei) show that surgical modifications
of the membrane pattern can be passed on for many generations even
though the organism's DNA has not been altered (Nanny 1983; Nelson,
Frankel, and Jenkins 1989). Wells
(MC) Page 64

So
there are clearly other factors involved in heredity and development
besides DNA. By itself this observation would not require the formulation
of a radically new theory of evolution. Although it is incompatible
with reductionistic, DNA-based neo-Darwinism, it is not necessarily
incompatible with the more general notion of descent with modification.
Biologist Sydney Brenner, who originally coined the term "genetic
program," then later repudiated it for being too simplistic, did not
abandon his commitment to Darwinian evolution, much less its underlying
naturalism (Brenner 1973; Lewin 1984). Wells
(MC) Page 64

It seems unlikely
that such patterns could determine the final outcome of embryogenesis
without noticeably affecting the intervening stages. Yet similar sea
urchins can exhibit remarkable differences in cell fate determination
during early development.

If an organism
were a house, its DNA would specify the building materials, and the
inherited arrangement of its cytoskeleton, membrane and cytoplasm
would help to specify the order in which those materials are assembled.
But the floor plan is determined neither by the building materials
nor by the order in which they are assembled. Where then is the floor
plan of the organism?

Some as-yet-undiscovered
law of development may do for embryos what quantum mechanics does
for atoms and molecules.

A vague hint of
what is to come might be found in complexity theory, in which physicists
use the term attractor to describe stable points, curves or
surfaces toward which complex movements tend to gravitate. Wells (MC) Page 65

[ See pendulum
example ]

The sort of thinking
that could account for recent discoveries in comparative embryology
and open the way to future progress in biology is alien to neo-Darwinism.
Instead creative thinking is much more likely to flourish in an intellectual
environment in which organisms are regarded as designed. If an organism
is designed, then the idea for it preceded its existence, and formal
and final causes are real. To be sure, one can regard organisms as
designed and still try to treat them as molecules in motion; but one
is also liberated, even encouraged, to regard them as much more. Wells (MC) Page 66

Conclusion: toward a new paradigm

According
to Thomas Kuhn, science normally functions within a "paradigm," a
general theory that has successfully answered some important questions
and that lays out a research program for further investigation (Kuhn
1970). Typically the general theory integrates specific inferences
from various scientific disciplines and includes philosophical assumptions
as well. Thus the Ptolemaic paradigm that dominated Western science
until the sixteenth century integrated not only medieval astronomy
but also Aristotelian physics and a geocentric cosmology. Wells
(MC) Page 66

Neo-Darwinism integrates
data and inferences from a variety of scientific disciplines; it incorporates
philosophical assumptions (such as naturalism); and its research program
currently guides the work of most biologists. If Kuhn was correct,
we may expect to see Darwinian biologists, like Ptolemaic astronomers,
dealing with anomalous evidence by adding epicycles to their theory.

Anomalous evidence
From developmental biology has been accumulating at an accelerating
rate since 1980. The anomalies are not isolated results reported in
obscure publications; instead they have been reproduced in many reputable
laboratories and reported in the best peer-reviewed journals. In their
zeal to confirm neo-Darwinism, some of the most talented biologists
in the world have devoted years of work to analyzing the developmental
effects of homeotic genes or searching for them in every conceivable
type of organism. Each new discovery is featured prominently in the
scientific press and celebrated as another nail in the coffin of those
who oppose Darwinism. Ironically however, these new discoveries about
homeotic genes are subverting the paradigm that inspired them, because
as those genes turn out to be more and more universal, the control
they exercise in development of turns out to be less and less specific
and their origin more and more difficult to explain from a Darwinian
perspective. Neo-Darwinists are left with ad hoc speculations about
how homeotic gene sequences might have evolved before the adaptations
which they now control; but these are merely the epicycles of a dying
paradigm. Wells (MC) Page
67

The
new paradigm, it seems to me, will be based on design. A design paradigm
can account far better than naturalistic Darwinism for the origin
of complex genes and their presence in a wide variety of organisms.
A design paradigm can nurture this sort of formal and teleological
thinking that will enable biologists to discover the laws of development
that have so far eluded them. In order for a design paradigm to out-compete
Darwinism, however, it will have to be developed to the point where
it is philosophically rigorous and scientifically fruitful. I am confident
that this can be done and that this conference will be a giant step
in that direction. Wells
(MC) Page 68

Writer / Editor: Dr. T. Peterson, Director,
WindowView.org

(081904)

Quotations
from "Mere Creation" (MC) edited
by William A. Dembski are used by permission
of InterVarsity Press, P.O. Box 1400, Downers
Grove, IL 60515. www.ivpress.com All rights
reserved. No portion of this material may be
used without permission from InterVarsity Press.

For a general listing of books, visit the WindowView Book Page for: Science and Scripture .

References of Interest

Step Up To Life

Time spent looking ... through a window on life and choice ... brings the opportunity to see in a new light. The offer for you to Step Up To Life is presented on many of the web pages at WindowView. Without further explanation we offer you the steps here ... knowing that depending on what you have seen or may yet explore in the window ... these steps will be the most important of your life ...